We investigated the cellular expression of Ig allotypes, their altered phenotypic expression in cultured cells and in mutant Basilea rabbits that produce elevated levels of Lambda type light chains and an unusual K2 isotype. We showed that the sire of the Basilea mutant expressed two isotypic forms of Kappa light chains (K1,b9 and K2, bas) and that the mutant lost the trait of expression of normal K1, b9 protein. The DNA of the mutant rabbits still contains structural genes corresponding to contant regions of both K1,b9 and K2, bas isotypes. Although K1,b9 and K2, bas are probably closely linked structural genes, the trait of expression of the K2, bas isotype maps in our breeding studies as an allele at the b locus; no recombinants have been observed yet. Immunofluorescence studies of Basilea rabbits suggest that a b9-like light chain is produced by pre-B cells but not by plasma cells. We hypothesize that there is a structural defect in this light chain that diminishes or destroys its ability to function as part of an intact Ig. Allotype-specific probes were used to search for latent b5 allotype in the expressed mRNAs of b9 splenocytes that were cultured with LPS and anti-b9 in order to modulate their expression of Kappa light chains. The sensitivity of our original dot blot tests was increased in Northern blotting and S1 protection experiments yet not RNA with b5-encoding sequences was detected. Moreover, when the allotype-specific b5 probe was used in Southern analyses of DNAs from b9, bas and b5 animals, it detected the K1,b5 gene in b5 DNA only. Alternative explanations for the apparant expression of latent kappa allotypes at the protein level must be considered. We reexamined earlier protein sequence data in the light of our newly deduced protein sequences from cloned DNAs to obtain new insight into the structural basis for VHa allotypes. The allotypes differ at seven positions in framework one and ten positions in framework three; most alternative amino acids can be derived from each other by single base changes. We suggest that some reported latent VHa allotypes may have arisen by somatic mutations and gene-conversion-like events that altered germ-line genes for nominal allotypes.